From 1b98f07eacd89b4b56d383dbc0d207c4c87ed9c4 Mon Sep 17 00:00:00 2001 From: David Waterman Date: Tue, 7 Nov 2023 11:45:59 +0000 Subject: [PATCH] Fix spelling mistakes with codespell -w --skip "*.js,*.html,*.css,*.png,*.log" and then git add -p to pick the intended changes --- _sources/dials_scale_user_guide.rst.txt | 2 +- _sources/documentation/getting_started.txt | 2 +- _sources/documentation/installation_developer.txt | 2 +- _sources/documentation/tutorials/developer_tutorial.txt | 4 ++-- _sources/documentation/tutorials/metrology_corrections.txt | 2 +- .../tutorials/multi_crystal_symmetry_and_scaling.rst.txt | 2 +- .../documentation/tutorials/processing_in_detail_CCP4.txt | 2 +- .../tutorials/processing_in_detail_betalactamase.txt | 2 +- .../tutorials/processing_in_detail_tutorial.rst.txt | 2 +- .../tutorials/processing_in_detail_tutorial.txt | 2 +- _sources/ssx_processing_guide.rst.txt | 2 +- dials-1.14/_sources/dials_scale_user_guide.rst.txt | 6 +++--- .../documentation/tutorials/developer_tutorial.rst.txt | 4 ++-- .../documentation/tutorials/metrology_corrections.rst.txt | 2 +- .../tutorials/multi_crystal_symmetry_and_scaling.rst.txt | 6 +++--- .../tutorials/processing_in_detail_betalactamase.rst.txt | 2 +- .../processing_in_detail_betalactamase_dui.rst.txt | 2 +- .../tutorials/processing_in_detail_tutorial.rst.txt | 2 +- dials-2.2/_sources/dials_scale_user_guide.rst.txt | 2 +- .../documentation/tutorials/developer_tutorial.rst.txt | 4 ++-- .../documentation/tutorials/metrology_corrections.rst.txt | 2 +- .../tutorials/multi_crystal_symmetry_and_scaling.rst.txt | 2 +- .../tutorials/processing_in_detail_betalactamase.rst.txt | 2 +- .../processing_in_detail_betalactamase_dui.rst.txt | 2 +- 24 files changed, 31 insertions(+), 31 deletions(-) diff --git a/_sources/dials_scale_user_guide.rst.txt b/_sources/dials_scale_user_guide.rst.txt index 08572c42c..2d866ccd5 100644 --- a/_sources/dials_scale_user_guide.rst.txt +++ b/_sources/dials_scale_user_guide.rst.txt @@ -82,7 +82,7 @@ To specify which intensity choice to use, there are a couple of options: **Adjusting the uncertainties/errors** All scaling programs adjust the uncertainties (sigmas) of the integrated data, to -account for additional systematic errors not suffiently modelled during integration. +account for additional systematic errors not sufficiently modelled during integration. :samp:`dials.scale` adjusts the intensity errors by refining a two-component error model (see the output log or :samp:`dials.scale.html` for the values). While this is an important correction and should improve the data quality for typical diff --git a/_sources/documentation/getting_started.txt b/_sources/documentation/getting_started.txt index 18e9859fb..3ec901223 100644 --- a/_sources/documentation/getting_started.txt +++ b/_sources/documentation/getting_started.txt @@ -88,7 +88,7 @@ Refinement The indexing includes refinement, but it is worth making an explicit refinement step in order to use all reflections in the dataset and optionally to refine a second time with a scan-varying crystal model before -integration. These two steps are therefor as follows:: +integration. These two steps are therefore as follows:: dials.refine experiments.json indexed.pickle dials.refine refined_experiments.json refined.pickle scan_varying=true diff --git a/_sources/documentation/installation_developer.txt b/_sources/documentation/installation_developer.txt index 2cfc0cde0..a9ed9fa22 100644 --- a/_sources/documentation/installation_developer.txt +++ b/_sources/documentation/installation_developer.txt @@ -103,7 +103,7 @@ installed on your machine: Before trying to compile anything, you will need to add the path to the hdf5.h file to the INCLUDE environment variable. If you don't have the INCLUDE -enviroment variable, just add it. You will also need a C/C++ compiler (e.g. +environment variable, just add it. You will also need a C/C++ compiler (e.g. visual sudio). Getting the CCTBX and DIALS sources diff --git a/_sources/documentation/tutorials/developer_tutorial.txt b/_sources/documentation/tutorials/developer_tutorial.txt index 45ccead60..4e3ba9298 100644 --- a/_sources/documentation/tutorials/developer_tutorial.txt +++ b/_sources/documentation/tutorials/developer_tutorial.txt @@ -91,7 +91,7 @@ partiality of reflections and computing the foreground/background mask. Of these the bounding box and mask methods are crucial for integration to work; partiality is currently only used in reporting and can be a placeholder. -The extention should have the ability to dump the profile model to phil +The extension should have the ability to dump the profile model to phil parameters so that it can be input via a profile.phil file to, for example, re-run integration with the same profile parameters. @@ -194,7 +194,7 @@ reflection list. .. +==========+============+===============================+ .. | 3d | rotation | 3D shoeboxes | .. +----------+------------+-------------------------------+ -.. | flat3d | rotation | 3D shoeboxes flattend | +.. | flat3d | rotation | 3D shoeboxes flattened | .. +----------+------------+-------------------------------+ .. | 2d | rotation | 2D partials | .. +----------+------------+-------------------------------+ diff --git a/_sources/documentation/tutorials/metrology_corrections.txt b/_sources/documentation/tutorials/metrology_corrections.txt index 8bc6e5f6a..c04ac1b12 100644 --- a/_sources/documentation/tutorials/metrology_corrections.txt +++ b/_sources/documentation/tutorials/metrology_corrections.txt @@ -952,7 +952,7 @@ shifts and mis-orientations has improved the overall profile fitting mean :math:`\frac{I}{\sigma_I}` and correlation coefficients. However, comparing the tables of results binned by resolution we see that the improvements are limited to the low resolution, and the results are worse at high resolution. For example, -we can make a quick plot of the profile fitting correlation coeffients. +we can make a quick plot of the profile fitting correlation coefficients. .. image:: /figures/CC_metrology_comparison.png diff --git a/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt b/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt index 554924e43..8c2bb948f 100644 --- a/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt +++ b/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt @@ -220,7 +220,7 @@ one would probably proceed with the first three datasets:: We could have also excluded a subset of images, for example using the option :samp:`exclude_images=3:301:600` to exclude the last 300 images of dataset 3. This option could be used to exclude the end of a dataset that was showing -sigificant radiation damage, or if the crystal had moved out of the beam part-way +significant radiation damage, or if the crystal had moved out of the beam part-way through the measurement. It is also worth checking the assigned space group using :samp:`dials.symmetry`. diff --git a/_sources/documentation/tutorials/processing_in_detail_CCP4.txt b/_sources/documentation/tutorials/processing_in_detail_CCP4.txt index aaab90aad..833ee8b71 100644 --- a/_sources/documentation/tutorials/processing_in_detail_CCP4.txt +++ b/_sources/documentation/tutorials/processing_in_detail_CCP4.txt @@ -430,7 +430,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/_sources/documentation/tutorials/processing_in_detail_betalactamase.txt b/_sources/documentation/tutorials/processing_in_detail_betalactamase.txt index 757290c04..6086fd159 100644 --- a/_sources/documentation/tutorials/processing_in_detail_betalactamase.txt +++ b/_sources/documentation/tutorials/processing_in_detail_betalactamase.txt @@ -440,7 +440,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt b/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt index 443322ac8..68fa2f134 100644 --- a/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt +++ b/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt @@ -358,7 +358,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and :math:`\phi` vary as a fuction of :math:`\phi`. + residuals in each of X, Y, and :math:`\phi` vary as a function of :math:`\phi`. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/_sources/documentation/tutorials/processing_in_detail_tutorial.txt b/_sources/documentation/tutorials/processing_in_detail_tutorial.txt index a932cbe73..3de79a77e 100644 --- a/_sources/documentation/tutorials/processing_in_detail_tutorial.txt +++ b/_sources/documentation/tutorials/processing_in_detail_tutorial.txt @@ -351,7 +351,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and :math:`\phi` vary as a fuction of :math:`\phi`. + residuals in each of X, Y, and :math:`\phi` vary as a function of :math:`\phi`. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/_sources/ssx_processing_guide.rst.txt b/_sources/ssx_processing_guide.rst.txt index 5d5bf03c3..677551f0e 100644 --- a/_sources/ssx_processing_guide.rst.txt +++ b/_sources/ssx_processing_guide.rst.txt @@ -112,7 +112,7 @@ During processing, data files will be created after each batch of crystals has been processed. The size of the batch for saving data can be set with the :samp:`batch_size` option. This creates numbered output files such as :samp:`integrated_0.refl, integrated_0.expt, integrated_1.refl, integrated_1.expt` etc. -After all images have been integated, unit cell clustering is performed and +After all images have been integrated, unit cell clustering is performed and reported, as this will have changed compared to at the end of indexing if using the ellipsoid integration algorithm. diff --git a/dials-1.14/_sources/dials_scale_user_guide.rst.txt b/dials-1.14/_sources/dials_scale_user_guide.rst.txt index 32b6bc49d..1139d35f0 100644 --- a/dials-1.14/_sources/dials_scale_user_guide.rst.txt +++ b/dials-1.14/_sources/dials_scale_user_guide.rst.txt @@ -72,13 +72,13 @@ whether the absorption term is suitable, as it may lead to overparameterisation. | if 25.0 <= oscillation range < 90.0 degrees; intervals 8.0, 10.0 | if oscillation range >= 90.0 degrees; intervals 15.0, 20.0 -These rules are designed to give a sensisble parameterisation, but not the +These rules are designed to give a sensible parameterisation, but not the best for a given dataset. All parameters are controllable when model is not auto. Excluding data/image handling after initial scaling ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -After a first round of scaling, it may be apparant that there are datasets, +After a first round of scaling, it may be apparent that there are datasets, or regions of datasets, that are in poor agreement with the rest of the dataset, and it would be advantageous to remove this data and rescale (this is particularly relevant for thin-wedge rotation datasets and still image datasets). @@ -143,7 +143,7 @@ across all resolution shells. In multi-dataset scaling, a separate selection is also made to find reflection groups that have a high connectedness across the datasets (choosing from groups with an average I/sigma above a cutoff). The parameters of the algorithm are therefore controllable with the following -options, if one explicity chooses :samp:`reflection_selection.method=quasi_random`: +options, if one explicitly chooses :samp:`reflection_selection.method=quasi_random`: :samp:`quasi_random.min_per_area`, :samp:`quasi_random.n_resolution_bins`, :samp:`quasi_random.multi_dataset.min_per_dataset` and :samp:`quasi_random.multi_dataset.Isigma_cutoff`. The :samp:`auto` option sets these diff --git a/dials-1.14/_sources/documentation/tutorials/developer_tutorial.rst.txt b/dials-1.14/_sources/documentation/tutorials/developer_tutorial.rst.txt index 26984e148..085beecde 100644 --- a/dials-1.14/_sources/documentation/tutorials/developer_tutorial.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/developer_tutorial.rst.txt @@ -91,7 +91,7 @@ partiality of reflections and computing the foreground/background mask. Of these the bounding box and mask methods are crucial for integration to work; partiality is currently only used in reporting and can be a placeholder. -The extention should have the ability to dump the profile model to phil +The extension should have the ability to dump the profile model to phil parameters so that it can be input via a profile.phil file to, for example, re-run integration with the same profile parameters. @@ -194,7 +194,7 @@ reflection list. .. +==========+============+===============================+ .. | 3d | rotation | 3D shoeboxes | .. +----------+------------+-------------------------------+ -.. | flat3d | rotation | 3D shoeboxes flattend | +.. | flat3d | rotation | 3D shoeboxes flattened | .. +----------+------------+-------------------------------+ .. | 2d | rotation | 2D partials | .. +----------+------------+-------------------------------+ diff --git a/dials-1.14/_sources/documentation/tutorials/metrology_corrections.rst.txt b/dials-1.14/_sources/documentation/tutorials/metrology_corrections.rst.txt index 8bc6e5f6a..c04ac1b12 100644 --- a/dials-1.14/_sources/documentation/tutorials/metrology_corrections.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/metrology_corrections.rst.txt @@ -952,7 +952,7 @@ shifts and mis-orientations has improved the overall profile fitting mean :math:`\frac{I}{\sigma_I}` and correlation coefficients. However, comparing the tables of results binned by resolution we see that the improvements are limited to the low resolution, and the results are worse at high resolution. For example, -we can make a quick plot of the profile fitting correlation coeffients. +we can make a quick plot of the profile fitting correlation coefficients. .. image:: /figures/CC_metrology_comparison.png diff --git a/dials-1.14/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt b/dials-1.14/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt index 6ddcce9af..54c705750 100644 --- a/dials-1.14/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt @@ -168,7 +168,7 @@ From the output, you can see that the merging statistics are significantly bette than before, with high correlation coefficients close to 1. At this point we could also apply a resolution limit by supplying :samp:`d_min=` to :samp:`dials.scale`, however the correlation coefficient and I/sigma looks good out to the highest -resolution so it is unneccesary in this case. +resolution so it is unnecessary in this case. To get a useful summary report, we can generate a dials-report or a xia2-report:: @@ -221,13 +221,13 @@ a string of integers ('0', '1', '2' ... based on the order of input):: We could have also excluded a subset of images, for example using the option :samp:`exclude_images=3:301:600` to exclude the last 300 images of dataset 3. This option could be used to exclude the end of a dataset that was showing -sigificant radiation damage, or if the crystal had moved out of the beam part-way +significant radiation damage, or if the crystal had moved out of the beam part-way through the measurement. Looking at the output from :samp:`dials.scale`, the merging statistics have significantly improved again, and although the multiplicity has reduced, we have not sacrificed much completeness. The anomalous correlation has only now -become apparant, so maybe it would be best to proceed with only these three +become apparent, so maybe it would be best to proceed with only these three datasets for structure solution. .. _Pointless: http://www.ccp4.ac.uk/html/pointless.html diff --git a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt index c477d15bc..419d1983b 100644 --- a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt @@ -595,7 +595,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt index 58091be1f..744c01ad2 100644 --- a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt @@ -334,7 +334,7 @@ Other useful plots in the report are: * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt index 46833ec99..672b97242 100644 --- a/dials-1.14/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt +++ b/dials-1.14/_sources/documentation/tutorials/processing_in_detail_tutorial.rst.txt @@ -351,7 +351,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and :math:`\phi` vary as a fuction of :math:`\phi`. + residuals in each of X, Y, and :math:`\phi` vary as a function of :math:`\phi`. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/dials-2.2/_sources/dials_scale_user_guide.rst.txt b/dials-2.2/_sources/dials_scale_user_guide.rst.txt index 8ae80c651..a0cc9121a 100644 --- a/dials-2.2/_sources/dials_scale_user_guide.rst.txt +++ b/dials-2.2/_sources/dials_scale_user_guide.rst.txt @@ -202,7 +202,7 @@ across all resolution shells. In multi-dataset scaling, a separate selection is also made to find reflection groups that have a high connectedness across the datasets (choosing from groups with an average I/sigma above a cutoff). The parameters of the algorithm are therefore controllable with the following -options, if one explicity chooses :samp:`reflection_selection.method=quasi_random`: +options, if one explicitly chooses :samp:`reflection_selection.method=quasi_random`: :samp:`quasi_random.min_per_area`, :samp:`quasi_random.n_resolution_bins`, :samp:`quasi_random.multi_dataset.min_per_dataset` and :samp:`quasi_random.multi_dataset.Isigma_cutoff`. The :samp:`auto` option sets these diff --git a/dials-2.2/_sources/documentation/tutorials/developer_tutorial.rst.txt b/dials-2.2/_sources/documentation/tutorials/developer_tutorial.rst.txt index 26984e148..085beecde 100644 --- a/dials-2.2/_sources/documentation/tutorials/developer_tutorial.rst.txt +++ b/dials-2.2/_sources/documentation/tutorials/developer_tutorial.rst.txt @@ -91,7 +91,7 @@ partiality of reflections and computing the foreground/background mask. Of these the bounding box and mask methods are crucial for integration to work; partiality is currently only used in reporting and can be a placeholder. -The extention should have the ability to dump the profile model to phil +The extension should have the ability to dump the profile model to phil parameters so that it can be input via a profile.phil file to, for example, re-run integration with the same profile parameters. @@ -194,7 +194,7 @@ reflection list. .. +==========+============+===============================+ .. | 3d | rotation | 3D shoeboxes | .. +----------+------------+-------------------------------+ -.. | flat3d | rotation | 3D shoeboxes flattend | +.. | flat3d | rotation | 3D shoeboxes flattened | .. +----------+------------+-------------------------------+ .. | 2d | rotation | 2D partials | .. +----------+------------+-------------------------------+ diff --git a/dials-2.2/_sources/documentation/tutorials/metrology_corrections.rst.txt b/dials-2.2/_sources/documentation/tutorials/metrology_corrections.rst.txt index bc6bb678d..85121afd9 100644 --- a/dials-2.2/_sources/documentation/tutorials/metrology_corrections.rst.txt +++ b/dials-2.2/_sources/documentation/tutorials/metrology_corrections.rst.txt @@ -952,7 +952,7 @@ shifts and mis-orientations has improved the overall profile fitting mean :math:`\frac{I}{\sigma_I}` and correlation coefficients. However, comparing the tables of results binned by resolution we see that the improvements are limited to the low resolution, and the results are worse at high resolution. For example, -we can make a quick plot of the profile fitting correlation coeffients. +we can make a quick plot of the profile fitting correlation coefficients. .. image:: /figures/CC_metrology_comparison.png diff --git a/dials-2.2/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt b/dials-2.2/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt index 5d38be633..d97b12777 100644 --- a/dials-2.2/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt +++ b/dials-2.2/_sources/documentation/tutorials/multi_crystal_symmetry_and_scaling.rst.txt @@ -213,7 +213,7 @@ one would probably proceed with the first three datasets:: We could have also excluded a subset of images, for example using the option :samp:`exclude_images=3:301:600` to exclude the last 300 images of dataset 3. This option could be used to exclude the end of a dataset that was showing -sigificant radiation damage, or if the crystal had moved out of the beam part-way +significant radiation damage, or if the crystal had moved out of the beam part-way through the measurement. It is also worth checking the assigned space group using :samp:`dials.symmetry`. diff --git a/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt b/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt index 8307c7bd2..7e5a846c8 100644 --- a/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt +++ b/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase.rst.txt @@ -563,7 +563,7 @@ Some of the most useful plots are * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines. diff --git a/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt b/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt index ca5cc00b2..da4abbb1f 100644 --- a/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt +++ b/dials-2.2/_sources/documentation/tutorials/processing_in_detail_betalactamase_dui.rst.txt @@ -335,7 +335,7 @@ Other useful plots in the report are: * **Difference between observed and calculated centroids vs phi**, which shows how the average - residuals in each of X, Y, and φ vary as a fuction of φ. + residuals in each of X, Y, and φ vary as a function of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines.